[2018-10-13 16:12:03] Beginning TopHat run (v2.1.1)
-----------------------------------------------
[2018-10-13 16:12:03] Checking for Bowtie
		  Bowtie version:	 2.2.2.0
[2018-10-13 16:12:03] Checking for Bowtie index files (genome)..
[2018-10-13 16:12:03] Checking for reference FASTA file
[2018-10-13 16:12:03] Generating SAM header for Bowtie2Index/genome
[2018-10-13 16:12:05] Reading known junctions from GTF file
[2018-10-13 16:12:07] Preparing reads
	 left reads: min. length=100, max. length=100, 75876 kept reads (189 discarded)
	right reads: min. length=100, max. length=100, 75778 kept reads (287 discarded)
[2018-10-13 16:12:09] Building transcriptome data files /scratch/8793347.1.p16/tophat2/tmp/RefSeq_GeneBody
[2018-10-13 16:12:19] Building Bowtie index from RefSeq_GeneBody.fa
[2018-10-13 16:17:01] Mapping left_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:17:10] Mapping right_kept_reads to transcriptome RefSeq_GeneBody with Bowtie2 
[2018-10-13 16:17:18] Resuming TopHat pipeline with unmapped reads
[2018-10-13 16:17:18] Mapping left_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:17:27] Mapping left_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:17:30] Mapping left_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:17:35] Mapping left_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:17:38] Mapping left_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:17:42] Mapping right_kept_reads.m2g_um to genome genome with Bowtie2 
[2018-10-13 16:17:51] Mapping right_kept_reads.m2g_um_seg1 to genome genome with Bowtie2 (1/4)
[2018-10-13 16:17:54] Mapping right_kept_reads.m2g_um_seg2 to genome genome with Bowtie2 (2/4)
[2018-10-13 16:17:58] Mapping right_kept_reads.m2g_um_seg3 to genome genome with Bowtie2 (3/4)
[2018-10-13 16:18:02] Mapping right_kept_reads.m2g_um_seg4 to genome genome with Bowtie2 (4/4)
[2018-10-13 16:18:06] Searching for junctions via segment mapping
[2018-10-13 16:19:13] Retrieving sequences for splices
[2018-10-13 16:20:20] Indexing splices
[2018-10-13 16:20:31] Mapping left_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:20:32] Mapping left_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:20:35] Mapping left_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:20:37] Mapping left_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:20:39] Joining segment hits
[2018-10-13 16:21:47] Mapping right_kept_reads.m2g_um_seg1 to genome segment_juncs with Bowtie2 (1/4)
[2018-10-13 16:21:49] Mapping right_kept_reads.m2g_um_seg2 to genome segment_juncs with Bowtie2 (2/4)
[2018-10-13 16:21:51] Mapping right_kept_reads.m2g_um_seg3 to genome segment_juncs with Bowtie2 (3/4)
[2018-10-13 16:21:53] Mapping right_kept_reads.m2g_um_seg4 to genome segment_juncs with Bowtie2 (4/4)
[2018-10-13 16:21:55] Joining segment hits
[2018-10-13 16:23:04] Reporting output tracks
-----------------------------------------------
[2018-10-13 16:24:14] A summary of the alignment counts can be found in /scratch/8793347.1.p16/tophat2/align_summary.txt
[2018-10-13 16:24:14] Run complete: 00:12:11 elapsed